The dead are not hard to find. Turn left into the desert after the town of Shiberghan and they lie all around - some in shallow graves, others protruding from the sand.

The clothes they wore are still there: decaying black turbans, charred shoes, a prayer cap, even a set of rusted car keys. In the nine months since they were buried the sun has bleached their bones white. But the jaws, femurs and ribs scattered across the desert are unmistakably human. We found teeth, thick black human hair and bits of skull.

There are a few clues to the prisoners' final moments: the site is littered with spent bullets. There are thick jackets lying above ground, which would have seemed useful to their owners last November, during the freezing desert nights.

Nobody knows exactly how many Taliban prisoners were secretly interred in this mass grave, a short distance from the main road. But there is now substantial evidence that the worst atrocity of last year's war in Afghanistan took place here; most controversially, during an operation masterminded by US special forces.

A 10-minute drive away is Shiberghan prison, where about 800 Taliban fighters who surrendered late last November at the town of Kunduz are held. The Afghan warlord General Abdul Rashid Dostum controls the prison; his mansion is nearby.

It was his commanders who transported the Taliban captives to Shiberghan. "It was awful. They crammed us into sealed shipping containers," a 24-year-old survivor, Irfan Azgar Ali, told the Guardian. "We had no water for 20 hours. We banged on the side of the container. There was no air and it was very hot.

"There were 300 of us in my container. By the time we arrived in Shiberghan, only 10 of us were still alive."

The prisoners still in Shiberghan - half of them Afghans, and half Pakistanis - estimate that about 400 people suffocated to death during the journey. Other sources say the figure is between 900 and 1,000. The Physicians for Human Rights group from Boston, which identified the mass grave earlier this year and later sent out a forensic scientist to carry out further tests, suggests that 2,000-3,000 of the 8,000 prisoners taken to Shiberghan died on the way.

But the Guardian has obtained harrowing details which suggest that their death was not a tragic accident but a deliberate act of revenge.

Some of the first Taliban fighters to surrender made the initial part of the journey in open lorries, their faces caked with dust. When they reached Mazar-i-Sharif, 90 miles from Kunduz, they were taken to Qala Zaini, a mud-walled fortified compound on the outskirts of the city. There Gen Dostum's soldiers crammed them into shipping containers. When they protested that they could not breathe, the soldiers told them to duck down, then fired several Kalashnikov rounds into the containers.

"I saw blood coming out of the holes," an eyewitness who refuses to be identified said.

A driver who made four trips to Dasht-i-Leili said not all the prisoners in his lorry were dead when they arrived: some were merely unconscious or gravely injured. The guards laid the dead and the still living out on the desert. "They raked them all with bullets to make sure they were dead," the driver said. "Then they buried them."

Last week Gen Dostum, now deputy defence minister in the new Afghan government, angrily denied accusations of human rights abuses, and pointed out that the Taliban had used shipping containers on numerous occasions to murder their enemies. He admitted that 200 prisoners had died, but said that most of the deaths were "due to wounds suffered in the fighting, but also due to disease, suffocation, suicide and a general weakness after weeks of intense fighting and bombardment".

In a joint statement with three other northern alliance commanders, he added: "There was no intentional killing."

What makes this massacre different from atrocities carried out by the Taliban regime is the presence of US special forces in the area, both at Shiberghan and at Erganak, 200 miles away, where the Taliban prisoners were first loaded into lorries. The question human rights groups want answered is: how much did the American soldiers know at the time?

The Pentagon said last week that the US troops had reported that they were unaware what had happened to the prisoners. But the evidence suggests that they were so close to Gen Dostum's soldiers that they may have been informed.

The general has been on the US payroll for nearly a year. According to Newsweek magazine, an elite team from the Fifth Special Forces Group first met up with Gen Dostum last October, when its members were dropped by Chinook helicopter at his mountain base.

They coordinated the Northern Alliance's dramatic assault on Mazar-i-Sharif, which fell on November 6, and then pursued the Taliban's northern army to Kunduz, where it remained trapped for more than two weeks. During this bloody period the US special forces unit, the 595 A-team, paid repeated visits to Shiberghan prison - plucking the American Taliban fighter John Walker Lindh, for example, from his cell hours after his detention.

Mr Lindh and the other 85 Taliban survivors from the Qala-i-Jhangi were also transported to Shiberghan by container, despite the intervention of the International Committee of the Red Cross.

One source claims that a dust-covered special forces vehicle pulled up at Dasht-i-Leili and parked on the side of the road, 500 metres from where bulldozers were busy burying the Taliban dead. Gen Dostum's soldiers instructed local villagers to stay away from the area.

Afghanistan's president, Hamid Karzai, has called for an inquiry into the massacre, which appears to have taken place at night. Last week he sent a team to investigate. But given Mr Karzai's tenuous grip on power, the team is unlikely to come to any definite conclusions.

The defence minister, Mohammad Fahim, has already dismissed the allegations of a massacre as a mere "rumour". Other senior figures in Mr Karzai's feuding administration have hinted that, given the Taliban's horrific record, the prisoners had it coming.

The issue is a difficult one, Omar Samad, the government's foreign ministry spokesman, said yesterday.

"We are very aware that the allegations need to be looked at thoroughly," he said. "But you have to bear in mind the overall context of what happened in Afghanistan over the past two decades. We are dealing with incidents of massacres, human rights violations and foreign militants entering Afghanistan ... which have built a sense of revenge that needs to be subdued."

A confidential UN memo obtained by Newsweek concluded that there was enough evidence to justify a "fully-fledged criminal investigation". But earlier this week Lakhdar Brahimi, the UN special envoy, said the government was too fragile to investigate further. "Politics is the art of the possible," he said.

The Pentagon has so far declined to answer several tricky questions, among them, were US soldiers present when the containers were first opened at Shiberghan prison?

US intelligence officers spent weeks interrogating Taliban and al-Qaida suspects at the jail, and in time removed 114 prisoners from their cramped, lice-ridden cells to Guantanamo Bay, Cuba, where they remain without charge.

But the same soldiers appear to have no knowledge of the mass grave just down the road.

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